RegulonDB RegulonDB 10.8: Gene Form
   

amiD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybjT ybjS amiD ybjP ybjQ anti-anti-terminator anti-terminator terminator ybjSp3 ybjSp3 TSS_1021 (cluster) TSS_1021 (cluster) ybjPp ybjPp TSS_1020 (cluster) TSS_1020 (cluster) TSS_1019 TSS_1019 ybjQp ybjQp TSS_1017 TSS_1017

Gene      
Name: amiD    Texpresso search in the literature
Synonym(s): ECK0858, G6452, b0867, ybjR
Genome position(nucleotides): 904913 --> 905743 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.08
External database links:  
ASAP:
 ABE-0002947
ECHOBASE:
 EB3451
OU-MICROARRAY:
 b0867
PortEco:
 amiD
STRING:
 511145.b0867
COLOMBOS: amiD


Product      
Name: N-acetylmuramoyl-L-alanine amidase D
Synonym(s): AmiD, YbjR
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 31.072
Isoelectric point: 7.775
Motif(s):
 
Type Positions Sequence
1 -> 16 MRRFFWLVAAALLLAG
17 -> 276 CAGEKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD
51 -> 52 YT
42 -> 179 PRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGP

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
  6 - cell structure --> 6.1 - membrane
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0019867 - outer membrane
GO:0016020 - membrane
molecular_function GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity
GO:0009392 - N-acetyl-anhydromuramoyl-L-alanine amidase activity
biological_process GO:0009254 - peptidoglycan turnover
GO:0009253 - peptidoglycan catabolic process
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Kerff F., et al., 2010
[2] Pennartz A., et al., 2009
External database links:  
ECOCYC:
 G6452-MONOMER
ECOLIWIKI:
 b0867
INTERPRO:
 IPR002502
INTERPRO:
 IPR036505
INTERPRO:
 IPR036365
INTERPRO:
 IPR036366
MODBASE:
 P75820
PDB:
 3D2Z
PDB:
 3D2Y
PDB:
 2BH7
PDB:
 2WKX
PFAM:
 PF01510
PRIDE:
 P75820
PRODB:
 PRO_000022093
PROSITE:
 PS51257
REFSEQ:
 NP_415388
SMART:
 SM00644
SMR:
 P75820
SWISSMODEL:
 P75820
UNIPROT:
 P75820


Operon      
Name: ybjQ-amiD         
Operon arrangement:
Transcription unit        Promoter
ybjQ-amiD


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1017 904477 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1019 904520 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1020 (cluster) 904522 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_1021 (cluster) 904530 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter ybjSp3 906898 reverse Similarity to the consensus
Read more > 		[ICWHO] [4]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Kerff F., Petrella S., Mercier F., Sauvage E., Herman R., Pennartz A., Zervosen A., Luxen A., Frere JM., Joris B., Charlier P., 2010, Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family., J Mol Biol 397(1):249-59

 [2] Pennartz A., Genereux C., Parquet C., Mengin-Lecreulx D., Joris B., 2009, Substrate-induced inactivation of the Escherichia coli AmiD N-acetylmuramoyl-L-alanine amidase highlights a new strategy to inhibit this class of enzyme., Antimicrob Agents Chemother 53(7):2991-7

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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